History

1.3.0 (2025-11-23)

  • Test Coverage Improvements - Improved overall test coverage from 89% to 91%: * Fixed stack_to_zarr.py coverage from 38% to 94% by adding tifffile to test dependencies * Improved base.py coverage from 82% to 99% * Improved qlty2DLarge.py coverage to 100% (removed test function from production code) * Added comprehensive tests for qlty2DLarge and qlty3DLarge modules * Fixed CI coverage reporting to use coverage run directly for better accuracy

  • Code Quality - Removed test/example functions from production modules

  • CI/CD - Enhanced dependency verification and coverage reporting in CI workflows

1.2.3 (2025-11-23)

  • New: 2.5D Quilt Module - Added NCZYX25DQuilt class for converting 3D volumetric data (N, C, Z, Y, X) into 2.5D multi-channel data by slicing the Z dimension into channels. Supports flexible channel specifications (identity, mean, std operations), selective z-slice processing, and two accumulation modes (2D planes or 3D stack).

  • New: Backend System - Added comprehensive backend support for various data sources: * InMemoryBackend: Wraps torch.Tensor for in-memory data * ZarrBackend: On-demand loading from OME-Zarr files * HDF5Backend: On-demand loading from HDF5 datasets * MemoryMappedBackend: Memory-mapped numpy arrays * TensorLike3D: Unified tensor-like interface for all backends * Convenience functions: from_zarr(), from_hdf5(), from_memmap()

  • New: Image Stack to Zarr Utility - Added stack_files_to_zarr() function in qlty.utils.stack_to_zarr for converting image file stacks (TIFF, PNG, etc.) into efficient Zarr format with automatic pattern matching, gap detection, and metadata storage.

  • New: False Color Visualization - Added FalseColorGenerator class in qlty.utils.false_color_2D for creating UMAP-based false-color visualizations of 2D images using patch-based dimensionality reduction.

  • Improved Test Coverage - Added 65+ new tests across qlty2_5D, backends_2_5D, and stack_to_zarr modules, significantly improving coverage: * qlty2_5D.py: 75% → 88% coverage * backends_2_5D.py: 62% → 70% coverage * stack_to_zarr.py: 38% → 94% coverage

  • CI Improvements - Fixed coverage reporting in CI by using coverage run directly instead of pytest-cov to avoid torch import conflicts. Added coverage verification steps.

1.2.0 (2025-11-13)

  • Added optional rotation-aware extraction for 2D patch pairs with matching overlap handling.

  • Expanded tests and documentation to cover rotated patch workflows.

1.1.0 (2025-11-12)

  • Restored Numba acceleration for 2D quilting via color-based parallel stitching that avoids write races.

  • Expanded 3D patch-pair sampling tests to cover edge cases and fallback logic, driving coverage to 100%.

  • Updated documentation to describe partially overlapping patch-pair utilities.

  • Noted that NCZYXQuilt and the Large* variants still need analogous race-free acceleration.

0.1.0 (2021-10-20)

  • First release on PyPI.

0.1.1 (some time ago)

  • Minor bug fixes

0.1.2. (2022-9-13)

  • Support for N-channel 3D tensors

  • On disc-accmulation for large datasets

0.1.3. (2022-9-13)

  • Cleanup and ready to redistribute

0.1.4. (2023-8-28)

  • Bug fix / behavoir change

0.1.5. (2023-12-28)

  • Changes to qlty3DLarge: bug fixes normalizing / averaging now done by dask

0.1.6. (2024-03-10)

bug fixes

0.1.7. (2024-03-12)

  • bug fix in border tensor definition.

0.2.0. (2024-03-12)

  • bug fixes

  • 2DLarge, mimics 3DLarge